I am writing a HTML document with knitr. My settings are:
---
fontsize: 12pt
output:
html_document:
fig_height: 7
fig_width: 9
keep_md: yes
smart: no
---
```{r global_options, include = FALSE}
knitr::opts_chunk$set(comment = NA)
```
I have a few code chunks that produce figures. Each of these chunks produces a single figure. I label the chunks with the understanding that, when I knit the document, the chunk labels become the file-names of the figures. For example, the chunk that I label "mtcar_histogram" should produce the file "mtcar_histogram.png".
But when I navigate to the "figure-html" sub-directory of the directory containing my document, I see that all the figures have an automatic numerical suffix. For example, I see "mtcar_histogram-1.png" instead of "mtcar_histogram.png".
When I checked the knitr options documentation, I read that:
"Note any number of plots can be recorded in a single code chunk, and this package does not need to know how many plots are in a chunk in advance -- it can figure out automatically, and name these images as fig.path-label-i where i is incremental from 1"
But as I stated earlier, none of my chunks produce multiple plots, so the numbering is un-necessary for me.
Is there a means of dis-abling the numbering?
Late answer, but might be useful. Taken from here:
https://github.com/yihui/knitr/issues/505
add this option to your setup chunk
knitr::opts_chunk$set(
fig.process = function(x) {
x2 = sub('-\\d+([.][a-z]+)$', '\\1', x)
if (file.rename(x, x2)) x2 else x
}
)
This will remove the suffix. To be used with caution.
Related
I am changing the font of a figure caption in my R Markdown and am using bookdown and pandoc to do so. My question is closely related to: How to change the figure caption format in bookdown?. I was able to get correct figure numbering and was able to alter the format of the "Figure 1" portion of the caption. However, I cannot figure out how to remove the colon in the output (i.e., "Figure 1:. ").
Minimal Example
Pandoc Function (taken from here)
function Image (img)
img.caption[1] = pandoc.Strong(img.caption[1])
img.caption[3] = pandoc.Strong(img.caption[3])
img.caption[4] = pandoc.Strong(". ")
return img
end
To use function Image in the R Markdown, save the file as "figure_caption_patch.lua", which will be called in pandoc_args in the YAML metadata.
R Markdown
---
title: Hello World
author: "Somebody"
output:
bookdown::word_document2:
fig_caption: yes
number_sections: FALSE
pandoc_args: ["--lua-filter", "figure_caption_patch.lua"]
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Test
Some text (Figure \#ref(fig:Xray)). Some text followed by a figure:
```{r Xray, fig.cap="Single-crystal X-ray structure of some text", echo=FALSE}
plot(cars)
```
Output
Figure 1:. This is a caption.
Desired Output
Figure 1. This is a caption.
In the pandoc function, I tried to subset the string of img.caption[3], but it did not work. I tried the following:
img.caption[3] = pandoc.Strong(string.sub(img.caption[3], 1, 1))
I know that if I was using R, then I could do something like:
a = c("words", "again")
substring(a, 1, 1)[1]
#output
[1] "w"
But unsure, how to do this with pandoc.
Looks like there was a change in rmarkdown which adds a colon by default. Also the reason why the answer in the linked post does not work anymore. For more on this and a solution see https://community.rstudio.com/t/how-to-change-the-figure-table-caption-style-in-bookdown/110397.
Besides the solution offered there you could achieve your desired result by replacing the colon by a dot. Adapting the lua filter provided by https://stackoverflow.com/a/59301855/12993861 this could done like so:
function Image (img)
img.caption[1] = pandoc.Strong(img.caption[1])
img.caption[3] = pandoc.Strong(pandoc.Str(string.gsub(img.caption[3].text, ":", ".")))
return img
end
I am creating a .pdf using R Markdown. I would like to have a section of text in two column format, and then follow that with a graph (or table, photo, etc.) that takes up the entire width of the page, and then return to two column text. I am new at Markdown / LaTex / Pandoc and I cannot figure out how to do it.
This answer by #AlisonShelton appears to be what I want, but when I run it I get this error in the RStudo R Markdown console:
! Undefined control sequence.
l.87 \btwocol
pandoc.exe: Error producing PDF
Error: pandoc document conversion failed with error 43
I have successfully used this method by #scoa to make a two column .pdf, but I don't know how go back and forth between one and two columns using this.
Here is some sample code for testing purposes
---
title: "Test"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Two columns of text
This seciton should be in two column format.
Here are a bunch of ? to make it longer: ???????????????????????????????????????????????????????????????????????????????
????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
??????????????????????????????????????????????????????????????????????????????????????????????????????????????????
## Once column section.
This part should be the whole page width
```{r plot}
plot(rnorm(20),rnorm(20))
```
## Now 2 columns again
This section should go back to two columns !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
What you can do is first, to add -- as you stated -- pandoc_args: ... into your YAML header. Second, there are a few LaTeX solutions around (like this or this one) which won't work for RMarkdown. The only way I found so far is to use \onyecolumn / \twocolumn -- just with the drawback of the page breaks. But perhaps you can live with it until there's a better solution.
---
title: "Test"
output:
pdf_document:
pandoc_args: [
"-V", "classoption=twocolumn"
]
html_document: default
header-includes:
- \usepackage{lipsum} # just used for producing example text in document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## Two columns of text
\lipsum[1-7]
\onecolumn
## Once column section.
This part should be the whole page width
```{r plot}
plot(rnorm(20),rnorm(20))
```
\lipsum[1]
\twocolumn
## Now 2 columns again
This section should go back to two columns
\lipsum
\begin{table*}
This is nice, but won't work with R chunks or headers. And you'll have to format with LaTeX code (e.g. \textbf{Foo blaah}).
\lipsum[1]
\end{table*}
\lipsum
I created a custom function which sets mfrow to nxn and creates n^2 scatter plots, with multiple data sets on each plot, based on an input list of data frames. The signature of my plotting function looks like this:
plot.return.list<-function(df.list,num.plot,title)
Where df.list is my list of data frames, num.plot is the total number of plots to generate (used to set mfrow) and title is the overall plot title (the function generates titles for each individual sub-graph).
This creats plots fine when I run the function from the console. However, I'm trying to get this figure into a markdown document using RStudio, like so:
```{r, fig.height=6,fig.width=6}
plot.return.list(f.1.list,4,bquote(atop("Numerical Approximations vs Exact Soltuions for "
,dot(x)==-1*x*(t))))
```
Since I haven't set the echo option in my {r} statement, this prints both the plotting code as well as the plot itself. However, if my first line instead reads:
{r, fig.height=6,fig.width=6,echo=FALSE}
Then both the code AND the plot disappear from the final document.
How do I make the plot appear WITHOUT the code? According to the example RStudio gives, setting echo=FALSE should make the plot appear without the code, but that isn't the behavior I'm observing.
EDIT: I seem to have tracked my problem down to kable. Whether or not I'm making a custom plot-helper function, any call to kable kills my plot. This can be reproduced in a markdown:
---
title: "repro"
author: "Frank Moore-Clingenpeel"
date: "October 9, 2016"
output: pdf_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(knitr)
options(default=TRUE)
repro.df<-data.frame((0.1*1:10)%*%t(1:10))
```
```{r, echo=FALSE}
kable(repro.df)
```
```{r, fig.height=6,fig.width=6,echo=FALSE}
plot(repro.df[,1],repro.df[,2])
```
In this code, the plot won't plot because I have echo set to false; removing the flag makes the plot visible
Also note that in my repro code, kable produces a table with a bunch of garbage in the last line--I don't know why, but this isn't true for my full original code, and I don't think it's related to my problem.
Thanks for the reproducible example. From this I can see that the problem is you don't have a newline between your table chunk and your plot chunk.
If you were to knit this and examine the MD file produced by knit (or set html_document as your output format and have keep_md: true to look at it), you would see that the table code and plot code are not separated by any newline. Pandoc needs this to delimit the end of the table. Without it, it thinks your  is part of the table and hence puts it as a "junk line" in the table rather than an image on its own.
Just add a newline between the two chunks and you will be fine. (Tables need to be surrounded with blank lines).
(I know you are compiling to LaTeX so it may confuse you why I am talking about markdown. In case it does, when you do Rmd -> PDF, Rmarkdown uses knit to go from RMD to MD, and then pandoc to go from MD to tex. This is why you still need to make sure your markdown looks OK).
I am trying to write a report in rmarkdown and then use knitr to generate a pdf.
I want all the code to be pushed to the "End of the document", while just displaying results interweaved with my text. The echo='hold' option doesn't do this.
Section of my markdown file
Generate data
```{r chunk1,echo='hold',R.options=}
num_seq<-rnorm(100,0.2)
num_seq
```
We further report the mean of these numbers.
```{r,echo='hold' }
mean(num_seq)
```
I have tried to read the the relevant documentation found here http://yihui.name/knitr/options/, but I can't figure out how to do this.
I don't think echo='hold' is an option. Regardless, the trick is to use echo=FALSE where the code is included, and then re-use the same chunk name and use eval=FALSE where you want the code to be printed. (Other options in both locations are fine, but these two are the minimum required.)
The following evaluates the code (and optionally includes output from it) where the chunk is located, but doesn't include the code until you specify.
# Header 1
```{r chunk1, echo=FALSE}
x <- 1
x + 5
```
This is a test.
```{r chunk1, eval=FALSE}
```
Results in the following markdown:
Header 1
========
## [1] 6
This is a test.
x <- 1
x + 5
Edit: I use this frequently in R markdown documents with randomness: I store the random seed in the very beginning (whether I set it manually or just store the current random state for later reproduction) and display it in an annex/appendix:
# Header 1
```{r setseed, echo=FALSE, include=FALSE}
set.seed(seed <- sample(.Machine$integer.max, size=1))
seed
```
This is a test `r seed`.
# Annex A {-}
```{r showsetseed, ref.label='setseed', eval=FALSE}
```
```{r printseed, echo=FALSE}
seed
```
This example doesn't include the results with the original code chunk. Unfortunately, the results aren't stored, and if I set eval=TRUE when I use the same chunk name later, it will calculate and present a different seed. That's why the printseed block. The reason I explicitly "show" seed in the first setseed block is solely so that, in the annex, the showsetseed and printseed chunks flow well. (Otherwise, set.seed does not return a number, so it would have looked wierd.)
BTW: this second example uses ref.label, which Yihui documents here as a more general approach to chunk reuse.
BTW #2: when I said "store the random state", that's not completely correct ... I'm storing a randomly-generated seed. The random state itself is much larger than a single integer, of course. I don't want to anger the PRNG gods :-)
I'm writing an Rmd file, to be processed by knitr into HTML. It contains some R chunks that generate figures, which get stored as data URIs in HTML.
1) How do I add a caption to such an image? I'd like to have a caption that says something like "Figure 3: blah blah blah", where the "3" is automatically generated.
2) How do I later on reference this image, i.e., "as you can see in Figure 3, blah blah".
I'm late to the party, but I wanted to mention a small package I recently built to do figure captioning and cross-referencing with knitr. It is called kfigr and you can install it using devtools::install_github('mkoohafkan/kfigr'). It is still in active development but the main functionality is there. Be sure to check out the vignette, it shows some usage examples and defines some hooks for figure captions and anchors (I may later choose to have the package import knitr and define those hooks on load).
EDIT: kfigr is now available on CRAN!
You can create the figure numbers with a simple counter in R; see one example here. The problem is whether the markdown renderer will render the figure caption for you: R Markdown v1 won't, but v2 (based on Pandoc) will.
I do not know. There is no direct way to insert a label as an identifier for figures, so it is probably not possible to cross reference figures with pure Markdown. Once you've got issues like this, think (1) do I really need it? (2) if it is intended to be a document with a complicated structure, I think it is better to use LaTeX directly (Rnw documents).
Also very late to the party I changed Yihuis suggestion here that he also linked above to do referencing.
```{r functions, include=FALSE}
# A function for captioning and referencing images
fig <- local({
i <- 0
ref <- list()
list(
cap=function(refName, text) {
i <<- i + 1
ref[[refName]] <<- i
paste("Figure ", i, ": ", text, sep="")
},
ref=function(refName) {
ref[[refName]]
})
})
```
```{r cars, echo=FALSE, fig.cap=fig$cap("cars", "Here you see some interesting stuff about cars and such.")}
plot(cars)
```
What you always wanted to know about cars is shown in figure `r fig$ref("cars")`
One way to do both of these is described here: http://rmflight.github.io/posts/2012/10/papersinRmd.html
Another is described here (but I don't know if it does your #2). http://gforge.se/2014/01/fast-track-publishing-using-knitr-part-iii/
Another solution:
https://github.com/adletaw/captioner
From the README:
captioner() returns a captioner function for each set of figures, tables, etc. that you want to create. See the help files for more details.
For example:
> fig_nums <- captioner()
> fig_nums("my_pretty_figure", "my pretty figure's caption")
"Figure 1: my pretty figure's caption"
> fig_nums("my_pretty_figure", cite = TRUE)
I did both (figure numbers + references) with bookdown. I added in output section in the header of the file:
output:
bookdown::html_document2:
fig_caption : TRUE
Then I created a figure in a R code chunk like follows:
{r, my-fig-label,echo=F, eval=T, fig.align = 'center', fig.cap="This is my caption"}
knitr::include_graphics(here::here("images", "my_image.png"))
This produces an automatic number under your figure. You can refer to it with \#ref(fig:my-fig-label).
Using the official bookdown documentation 4.10 Numbered figure captions:
---
output: bookdown::html_document2
---
```{r cars, fig.cap = "An amazing plot"}
plot(cars)
```
```{r mtcars, fig.cap = "Another amazing plot"}
plot(mpg ~ hp, mtcars)
```